Could you try...

byte[] bytes = new byte[]{1,2,3,4,5,6,7,8,9}; 
String stringToStore = new String(Base64.encode(bytes));
byte[] restoredBytes = Base64.decode(stringToStore.getBytes()); 

Always double-quote your variables when you use them^*.

Repeatable example

myVar=$(perl -e 'print "hello, world. " x100, "\n"' | base64)
echo "$myVar"

echo $myVar | base64 --decode >/dev/null      # Fails
base64: invalid input

echo "$myVar" | base64 --decode >/dev/null    # Works

What's happening is that the quoted variable produces N lines of 76 characters, but the unquoted variable produces 1 line of 76 x N characters plus a space between each group of 76. This second output is not valid base64 format.

Reading comments and feedback, it seems that the source base64 data is still not completely compatible with the base64 command. In this instance it's necessary to skip unexpected characters:

printf '%s' "$myVar" | base64 --decode --ignore-garbage

Here I have also switched from using echo to printf (without a trailing newline) so that the output is better controlled.

^{* Except when you really know you have a necessary reason not to quote. These cases are few and far between. If in doubt, quote.}

From xxd's man page

xxd creates a hex dump of a given file or standard input.

You're taking a hex dump for the decoded value.

You can reproduce it with the utility provided here

System.out.println(Hex.encodeHexString(outAsByte));

generates

3ce353e2e6264d8c223f4a26700c591bc6b7bca2

which matches your

                  //  3ce353e2e6264d8c223f4a26700c591bc6b7bca2
String expectedOut = "3ce353e2e6264d8c223f4a26700c591bc6b7bca2";